rs7758893

chr6-89206922-C-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_002042.5(GABRR1):c.123-3437G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.801 in 152,118 control chromosomes in the GnomAD database, including 49,703 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.80 (49703 hom., cov: 32)
• Consequence: GABRR1 NM_002042.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.454

Genes affected

GABRR1 (HGNC:4090): (gamma-aminobutyric acid type A receptor subunit rho1) GABA is the major inhibitory neurotransmitter in the mammalian brain where it acts at GABA receptors, which are ligand-gated chloride channels. GABRR1 is a member of the rho subunit family. Several transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Feb 2012]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.898 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
GABRR1	NM_002042.5	c.123-3437G>A		intron_variant		ENST00000454853.7

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
GABRR1	ENST00000454853.7	c.123-3437G>A		intron_variant		1	NM_002042.5	P1

Frequencies

GnomAD3 genomes AF: 0.801 AC: 121684 AN: 152000 Hom.: 49650 Cov.: 32

Gnomad AFR AF: 0.905

Gnomad AMI AF: 0.774

Gnomad AMR AF: 0.712

Gnomad ASJ AF: 0.884

Gnomad EAS AF: 0.358

Gnomad SAS AF: 0.763

Gnomad FIN AF: 0.667

Gnomad MID AF: 0.810

Gnomad NFE AF: 0.810

Gnomad OTH AF: 0.794

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.801 AC: 121797 AN: 152118 Hom.: 49703 Cov.: 32 AF XY: 0.788 AC XY: 58589 AN XY: 74350

Gnomad4 AFR AF: 0.905

Gnomad4 AMR AF: 0.713

Gnomad4 ASJ AF: 0.884

Gnomad4 EAS AF: 0.358

Gnomad4 SAS AF: 0.763

Gnomad4 FIN AF: 0.667

Gnomad4 NFE AF: 0.810

Gnomad4 OTH AF: 0.793

Alfa AF: 0.804 Hom.: 62542

Bravo AF: 0.808

Asia WGS AF: 0.592 AC: 2063 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
Cadd	Benign	1.2
Dann	Benign	0.62

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs7758893; hg19: chr6-89916641; COSMIC: COSV65620841;